docs: add warning about object methods discarding refinements

[kevinmitch14]

This caught me. Refinement gets lost and validation passes

const testPayload = {
  name: "Test",
  items: [],
};

const baseSchema = z.object({
  id: z.string(),
  name: z.string(),
  items: z.string().array(),
});

const failingSchema = baseSchema
  .superRefine((val, ctx) => {
    if (val.items.length === 0) {
      ctx.addIssue({
        message: "Must have at least one item",
        code: "custom",
        path: ["items"],
      });
    }
  })
  .omit({ id: true });

You also mention it here: #4874

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